All GSMS courses
Only GSMS PhD students (including BCN PhD students) can participate in these courses. Use your P-number to register (ask your Personnel Office).
For registration please go to Upcoming courses.
Course: Single cell RNAseq data for beginners
This course although marked as “for beginners” implies that students have some elementary experience with R programming. Knowledge of the regular RNAseq analysis is an advantage.
In this course I will briefly mention the folllwing:
1. How traditional RNAseq analysis is done with limma, edgeR, deseq2. Next I will tell
2. How Single Cell protocols are organized in R, like Scater, Seurat, Monocle, what’s the difference
3. Major goals of a single cell protocols: Finding cell clusters, finding markers of clustered cells.
4. Introduction to a specific elements: pseudotiming, inferring differentiation patterns (a concept of velocity)
5. Predicting cell-signalling (CellChat, SingleCellSignal packages).
Intended for:
PhD students in biology, medical biology, medicine or farmacy- those who professionally connected to biology. Students should have an elementary knowledge of using R packages for the RNAseq analysis, preferably passed the course on “gene expression data for beginners” (or equivalent level). The course is practically oriented. It means students will exercise in writing R-scripts and analyzing the real expression data.
Assumed pre-knowledge
General knowledge of cell biology, regulation of a gene expression, and basics of R scripting is required.
Equipment
Students should have personal laptop with administrative rights (able to install software and packages) with 8 GM RAM at least. It is implied that students have already installed R and R-studio, have access to the internet.
Recommended
Students will be referred to online documentation of each package
Homework
Expect homework on discussed subjects. This will also form the basis to pass the course
Exam
90% participation required, 90% delivered homework required.
Course schedule:
5 times 2 hours each (9-11 a.m.). February - March
Minimally 10 students required. Maximum 20 students accepted.
During registration provide your @rug.nl accounts for the ease of the access to the google drive files.
EC (without exam)
0.5
Course coordinator
- Leonid Bystrykh, PhD
Language
English